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SIS Converter

Universal Converter for the Most Common Scientific Imaging File Formats

Using SIS Converter

Opening the arivis SIS Converter

  1. Execute arivis SIS Converter by clicking on the related icon on the desktop.
  2. The arivis SIS Converter dialog opens.

Importing files

  1. To import images, choose Add Files... from the main menu, or drag and drop files or folders onto an open arivis SIS Converter window. You will be guided through the import process and be able to work with your data after the import process finishes.
  2. The selected files are analyzed and, depending on the number and structure of the input files, a dialog box appears.
    If your import file is a single, simple image file, the following Import files dialog box is displayed:

    The imported file will be located at the displayed location.
  3. To change the destination file, modify the path manually or use the Browse button to display a file save dialog.
  4. Click on more options to change the Target Pixel Type or Show file information.

Modifying the list of files

  1. Open the Detailed file information dialog, which can be found under more options in every import dialog box, to modify the list of files for your import scenario.
  2. Remove files from the import list and freely change the order in which the input files are imported.

Complex Import

To import complex, unknown, image structures, select the Custom Import scenario.

It enables you to freely define your import scenario in detail. If the suggested scenarios do not fit your need, this dialog is your partner in defining your import scenario.

Arranging the order of the template elements

The order of the template elements defines in which order your input files are arranged dimensionally. Setting the time point dimension to a value of 5 means: Take every 5th image and add it to a new time point.

  1. Press Add Dimension to add a new selector to the current template.
  2. Click Remove to remove an element.
  3. Click Up or Down to change the order of the dimensions.
  4. Press Update preview to display a preview of how the current template affects your import scenario in the lower preview panel.
  5. To apply the current template and change your current mapping, press OK.

Pattern matching

Sometimes the filenames contain information that define on which dimension each image has to be located in the resulting image.

  1. Choose Selection > Pattern matching... to open the import pattern matching dialog. Here you can define a pattern that contains specific identifiers that mark parts of the input filename as a locator for an image dimension.
  2. The identifiers match numeric values (including leading zeros). Use the wildcard identifiers * and ? to ignore other numeric values. If your input files start counting a dimension at 100, Edit offsets helps you set a new start for counting. E.g. if your first input file is named "input_plane0100_frame010_channel01", and you don't adjust the offsets, your resulting file may contain empty data. To alleviate this change the plane offset to -100, the time point offset to -10, and the channel offset to -1. Now your resulting file will only contain the data you set up to import.
  3. Press the Refresh button to refresh the preview of how the current pattern affects your import scenario in the lower preview panel.

Detecting channel names

Sometimes the filenames contain information about channel names.

  1. Choose Selection > Detect Channel Names... to open the Detect Channel Names dialog box. Here you can define a pattern that matches a channel name and map it to a resulting channel.
    You can use this mechanism to import multiple input files with a single channel into a single file with multiple channels.
  2. If your import data contains more than one channel use Add to create another channel for your import result.
  3. Use Update preview to check, if your channel patterns match with your import data.

Saving import scenario definitions

  1. To store your import scenario definition, you need to open the Custom import dialog box by pressing More options... and Perform custom import....
  2. After checking that the mapping table reflects your import scenario, choose File > Save import scenario... in order to save this import scenario to a file on your computer.

Supported image formats

arivis SIS Converter supports a large number of image formats. Media handlers are extension plug-ins which enable arivis SIS Converter to import and export files in various file formats. For instance, the importers and exporters use these media handlers.

The following media-handlers are available in your arivis SIS Converter:

Amira-Mesh Media Handler

The Amira-Mesh media handler enables the import of Amira-Mesh files, containing uniform lattice data. Amira-Mesh files can contain different types of data, for instance spatial graphs or stacked lattices. This media handler is not able to read these special data types.

The Amira-Mesh media handler allows you to import images of the following file format: Amira-Mesh (*.am)

Aperio Media Handler

The Aperio media handler allows you to import images of the following file format: Aperio (JPEG) (*.svs) , Aperio JPEG2000) (*.svs)

Metamorph Media Handler

The Metamorph media handler is part of the Bio Media Handler Module which enables the import of some common image formats used in biology-related working areas.

The Metamorph media handler allows you to import images of the following file format: Metamorph (*.stk)

Hamamatsu Media Handler

The Hamamatsu media handler allows you to import images of the following file format: NDPI (*.ndpi) , Virtual Microscope Specimen (*.vms)

ICS Media Handler

The ICS media handler allows you to import images of the following file format: ICS 1.0 (*.ics) , ICS 2.0 (*.ids)

Imaris Media Handler

The Imaris media handler enables the import of the Bitplane Imaris file format (IMS). The Imaris media handler is using the HDF5 Library.

JPEG Media Handler

The JPEG media handler enables an optimized import of JPEG image files.

It allows you to import images of the following file format: JPEG (*.jpg, *.jpeg)

LSM Media Handler

The LSM media handler enables the import of the LSM file formats.

Mirax Media Handler

The Mirax media handler enables the import of the Mirax SlideAC file format. This image format originates from Carl Zeiss Mirax Slide scanner systems and is based on image pyramids.

The Mirax media handler allows you to import images of the following file format: Mirax SlideAC (*.mrxs)

NIfTI Media Handler

The NIfTI media handler enables the import of the NIfTI (Neuroimaging Informatics Technology Initiative) image file formats.

The NIfTI media handler allows you to import images of the following file formats: single-file(combined data and meta- data)(.nii) ,single-file gzip-compressed (.nii.gz) , dual- file(separate data and meta-data, respectively)(.img/.hdr)

Nikon Media Handler

The Nikon media handler enables the import of data created by the Nikon imaging solutions.

The Nikon media handler allows you to import images of the following file format: Nikon ND2 (*.nd2)

RAWInfo Media Handler

The RAWInfo media handler enables the import of raw image files by using a control (*.rawinfo) file that contains dimension information.

The Raw media handler allows you to import images of the following file formats: RawInfo (*.rawinfo)

Tiff Media Handler

The Tiff media handler enables the import of TIFF (Tagged Image File Format) based image file formats. TIFF is a commonly used format to store images.

The Tiff media handler allows you to import images of the following file formats: TIFF (*.tif, *.tiff) , OME TIFF (*.tif, *.tiff)

VOL Media Handler

The VOL media handler enables the import of VG Studio VOL images.

The VOL media handler allows you to import images of the following file format: VOL (*.vol/*.vgi)

To import a VG Studio VOL dataset both files (.vol & .vgi) are needed!

Zeiss ZVI Media Handler

The Zeiss ZVI media handler enables the import of Zeiss image data.

The Zeiss ZVI media handler allows you to import images of the following file formats: Zeiss ZVI (*.zvi) , Zeiss ZISRAW/CZI (*.czi)

Release Notes

SIS Converter (Pro) 4.1 Release

Announcing the latest release of the arivis SIS Converter and arivis SIS Converter Pro

Bugfixes

  • Pixel size for multiple image sets using custom import
  • CZI import with different pixel types (in one data set)
  • Possible problem with Nikon ND2 import for pre-stitched data
  • Avoid conversion history corruption
  • Small UI glitches
  • Separate Start Menu entries for the free and the pro version
  • Avoid infinite loop with the same source and destination folders (SIS Converter PRO)
  • Improved robustness for unexpected termination

DOWNLOAD FREE VERSION

 

Supported File Formats

Supported Image File Formats

SIS Converter and Converter Pro *as of Dec 2022*

  • Abberior Imspector (.obf, .msr)
  • AmiraMesh (*.am)
  • Aperio SVS (*.svs)
  • arivis Single Image Stack 3 (*.sis)
  • BigDataViewer file format (*.xml)
  • CompuServe GIF (*.gif, *.giff)
  • DeltaVision image file (*.dv)
  • DICOM Directory (*.dicomdir, *.DICOMDIR)
  • DICOM Image (*.dcm)
  • Fiji/ImageJ-TIFF (*.tif, *.tiff)
  • GE InCell (*.xdce)
  • Hamamatsu tiff-like file format (*.ndpi)
  • High Dynamic Range Image (*.hdr)
  • ICS 1.0/2.0 file format (*.ics, *.ibs)
  • Imaris IMS (*.ims)
  • Imspector (*.obf/*.msr)
  • JPEG/JFIF (*.jpg, *.jpeg, *.jif, *.jfif, *.j, *.jpe)
  • JPEG-2000 (*.jp2, *.j2k, *.j2c)
  • Leica Image File Format (*.lei,*.lif)
  • Luxendo images (saved as BigDataViewer *.xml)
  • Metamorph STK (*.stk)
  • Mirax SliceAC file format (*.mrxs)
  • Molecular Devices (GE IN Carta)
  • Neuroimaging Informatics Technology Initiative Image File Format (*.hdr, *.nii, *.nii.gz)
  • Nikon ND2 files (*.nd2)
  • Olympus file format (*.oir, *.oib, *.oif)
  • Olympus Media Handler (*.vsi)
  • OME-TIFF (*.tif, *.tiff)
  • OME-TIFF/FEI (*.tif, *.tiff)
  • OME-TIFF/LaVision (*.tif, *.tiff)
  • Perking Elmer PE (standard PE format, .qptiff  Columbus metadata)
  • Portable Network Graphics (*.png)
  • Slidebook (.sld) Media Handler
  • TIFF Tagged Image (*.tif, *.tim, *.tiff)
  • TillVision file formats (*.rbinf, *.ini)
  • TrakEM2 Image file format (trakem2.xml, *.xml)
  • VGI/VOL Media Handler
  • VG Studio Max (*.vgl)
  • VG Studio Images VOL Media Handler (*.vol, *.vgi)
  • Virtual Microscopy Specimen file format (*.vms, *.vmu)
  • Windows Bitmap (*.bmp, *.rle, *.vga, *.rl4, *.rl8, *.sys)
  • Zeiss Axiovision ZVI (*.zvi)
  • Zeiss CZI/ZISRAW (*.czi, *.zisraw)
  • Zeiss LSM-tiff (*.lsm)
  • Yokogawa CV (*.mlf)
  • Yokogawa CPf (*.mmd)

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